Visualize Tab
The Visualize tab provides different visualizations for structural events and Variant Allele Frequency (VAF) distribution through the following tabs:
Genome View
VAF Distribution
Genome View
The Genome View tab shows an overview of the following events:
Structural variants — Structural variants with VCF filter PASS by chromosomal position. The legend to the right of the genome view identifies the events (translocation, inversion, deletion, insertion, and tandem duplication). Translocations begin at the karyogram at the top of the track and connect to chromosomes identified at the bottom of the track.
Coverage and copy number variants — The depth of coverage by chromosomal position. Data points are color-coded by presence of copy number variant calls. The legend identifies the events (gain, gain LOH, neutral LOH, loss, and no call). Hovering over a region will highlight the copy number variant call and clicking provides variant details.
B-allele ratio — The B-allele ratio by chromosomal position. The B-allele ratio is the ratio of the two alleles A and B. Heterozygous regions have B-allele ratios that are around 0.5, whereas homozygous regions (such as through loss-of-heterozygousity) have B-allele ratios that are around 0.0 and 1.0.
Small variants - Small variants with VCF filter PASS by chromosomal position. Data points can be color-coded by variant type or substitution. Y-axis can display VAF or intermutational distance (requires sufficient zoom).
The Genome View can be shown in the following displays:
Linear plot - Chromosomes are arranged sequentially in a linear manner.
Circos plot - Chromosomes are arranged sequentially in a circular manner with translocations in the center ring.
Track availability depends on the VCFs provided by the secondary analysis pipeline.
For example,
If there's no structural variant VCF provided, then the structural variant track will not be available.
If there's no absolute copy number provided in the VCF, then the copy number variant track will not be available.
Example Linear Plot:
Example Circos Plot:
Navigation
Click on a chromosome to zoom into a chromosome.
Or use the Search field at the top of the section to search for a location by specifying one of the following:
Chromosome (for example, chr2)
Range (for example, chr2:0-24219350)
Position (for example, chr2:10000)
After entering search information, press Enter to view the location.
After clicking on a chromosome or searching for a location:
To pan, use the pan controls at the top of the section, or click and drag one of the tracks left or right.
To zoom, use the zoom controls at the top of the section, or hold ctrl and scroll with your mouse or trackpad.
To return to the all chromosomes view, remove any values from the Search field or type all and press Enter.
Open Variant Details
VAF Distribution
The VAF Distribution tab provides an overview of the VAF across the SNV and Delins variant types. Hover over the bars on the graph to show the number of variants associated with the VAF. The VAF is calculated as alt/(alt + ref), where alt and ref are the number of reads supporting the non-reference and reference bases. VAF depends on the following characteristics:
Tumor ploidy
Cancer heterogeneity
Copy number variations
You can also select Explain Plot to view this information.
The Variant Type drop-down list above the graph has two selectable options: SNV or Delins. The SNV option shows small variant SNVs with VCF filter PASS. The Delins option shows small variant delins, insertions, and deletions with VCF filter PASS.
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